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• Stenseth, Nils Christian; Tao, Yuxin; Zhang, Chutian; Bramanti, Barbara; Büntgen, Ulf & Cong, Xianbin [Show all 19 contributors for this article] (2022). No evidence for persistent natural plague reservoirs in historical and modern Europe. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 119(51). doi: 10.1073/pnas.2209816119. Full text in Research Archive
• Stenseth, Nils Christian; Dean, Katharine Rose & Bramanti, Barbara (2022). The End of Plague in Europe. Centaurus. Journal of the European Society for the History of Science. ISSN 0008-8994. 64(1), p. 61–72. doi: 10.1484/J.CNT.5.130126. Full text in Research Archive
• Bramanti, Barbara; Wu, Yarong; Yang, Ruifu; Cui, Yujun & Stenseth, Nils Christian (2021). Assessing the origins of the European Plagues following the Black Death: A synthesis of genomic, historical, and ecological information. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 118(36), p. 1–6. doi: 10.1073/pnas.2101940118. Full text in Research Archive
• Guellil, Meriam; Rinaldo, Natascia; Zedda, Nicoletta; Kersten, Oliver; Gonzalez Muro, Xabier & Stenseth, Nils Chr. [Show all 8 contributors for this article] (2021). Bioarchaeological insights into the last plague of Imola (1630–1632). Scientific Reports. ISSN 2045-2322. 11(1), p. 1–12. doi: 10.1038/s41598-021-98214-2. Full text in Research Archive
• Guellil, Meriam; Kersten, Oliver; Namouchi, Amine; Luciani, Stefania; Marota, Isolina & Arcini, Caroline [Show all 17 contributors for this article] (2020). A genomic and historical synthesis of plague in 18th century Eurasia. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 117(45), p. 28328–28335. doi: 10.1073/pnas.2009677117. Full text in Research Archive
• Ottoni, Claudio; Guellil, Meriam; Ozga, Andrew; Stone, Anne; Kersten, Oliver & Bramanti, Barbara [Show all 8 contributors for this article] (2019). Metagenomic analysis of dental calculus in ancient Egyptian baboons. Scientific Reports. ISSN 2045-2322. 9, p. 1–10. doi: 10.1038/s41598-019-56074-x. Full text in Research Archive Show summary

  Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals’ oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9th–6th centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons’ oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.

• Bramanti, Barbara; Dean, Katharine Rose; Walløe, Lars & Stenseth, Nils Christian (2019). The third plague pandemic in Europe. Proceedings of the Royal Society of London. Biological Sciences. ISSN 0962-8452. 286(1901), p. 1–8. doi: 10.1098/rspb.2018.2429. Full text in Research Archive
• Xu, Lei; Stige, Leif Christian; Leirs, Herwig; Neerinckx, Simon; Gage, Kenneth L. & Yang, Ruifu [Show all 13 contributors for this article] (2019). Historical and genomic data reveal the influencing factors on global transmission velocity of plague during the Third Pandemic. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 116(24), p. 11833–11838. doi: 10.1073/pnas.1901366116. Full text in Research Archive
• Bramanti, Barbara; Zedda, Nicoletta; Rinaldo, Natascia & Gualdi-Russo, Emanuela (2018). A critical review of anthropological studies on skeletons from European plague pits of different epochs. Scientific Reports. ISSN 2045-2322. 8(17655), p. 1–12. doi: 10.1038/s41598-018-36201-w. Full text in Research Archive
• Namouchi, Amine; Guellil, Meriam; Kersten, Oliver; Hänsch, Stephanie; Ottoni, Claudio & Schmid, Boris Valentijn [Show all 16 contributors for this article] (2018). Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 115(50), p. E11790–E11797. doi: 10.1073/pnas.1812865115. Full text in Research Archive Show summary

  Over the last few years, genomic studies on Yersinia pestis, the causative agent of all known plague epidemics, have considerably increased in numbers, spanning a period of about 5,000 y. Nonetheless, questions concerning historical reservoirs and routes of transmission remain open. Here, we present and describe five genomes from the second half of the 14th century and reconstruct the evolutionary history of Y. pestis by reanalyzing previously published genomes and by building a comprehensive phylogeny focused on strains attributed to the Second Plague Pandemic (14th to 18th century). Corroborated by historical and ecological evidence, the presented phylogeny, which includes our Y. pestis genomes, could support the hypothesis of an entry of plague into Western European ports through distinct waves of introduction during the Medieval Period, possibly by means of fur trade routes, as well as the recirculation of plague within the human population via trade routes and human movement.

• Guellil, Meriam; Kersten, Oliver; Namouchi, Amine; Bauer, Egil Lindhart; Derrick, Michael & Jensen, Anne Østergaard [Show all 8 contributors for this article] (2018). Genomic blueprint of a relapsing fever pathogen in 15th century Scandinavia. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 115(41), p. 10422–10427. doi: 10.1073/pnas.1807266115. Full text in Research Archive Show summary

  Louse-borne relapsing fever (LBRF) is known to have killed millions of people over the course of European history and remains a major cause of mortality in parts of the world. Its pathogen, Borrelia recurrentis, shares a common vector with global killers such as typhus and plague and is known for its involvement in devastating historical epidemics such as the Irish potato famine. Here, we describe a European and historical genome of B. recurrentis, recovered from a 15th century skeleton from Oslo. Our distinct European lineage has a discrete genomic makeup, displaying an ancestral oppA-1 gene and gene loss in antigenic variation sites. Our results illustrate the potential of ancient DNA research to elucidate dynamics of reductive evolution in a specialized human pathogen and to uncover aspects of human health usually invisible to the archaeological record.

• Dean, Katharine Rose; Krauer, Fabienne; Walløe, Lars; Lingjærde, Ole Christian; Bramanti, Barbara & Stenseth, Nils Christian [Show all 7 contributors for this article] (2018). Human ectoparasites and the spread of plague in Europe during the Second Pandemic. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 115(6), p. 1304–1309. doi: 10.1073/pnas.1715640115.
• Bramanti, Barbara; Stenseth, Nils Christian; Walløe, Lars & Xu, Lei (2016). Plague: A disease which changed the path of human civilication. In Yang, Ruifu & Anisimov, Andrey (Ed.), Yersinia pestis: Retrospective and perspective. Springer. ISSN 978-94-024-0888-1. p. 1–23. doi: 10.1007/978-024-0890-4_1.
• Hansch, Stephanie; Cilli, Elisabetta; Catalano, Giulio; Gruppiono, Giorgio; Bianucci, Raffaella & Stenseth, Nils Christian [Show all 8 contributors for this article] (2015). The pla gene, encoding plasminogen activator, is not specific to Yersinia pestis. BMC Research Notes. ISSN 1756-0500. 8(1). doi: 10.1186/s13104-015-1525-x.
• Schmid, Boris Valentijn; Büntgen, Ulf; Easterday, William Ryan; Ginzler, Christian; Walløe, Lars & Bramanti, Barbara [Show all 7 contributors for this article] (2015). Climate-driven introduction of the Black Death and successive plague reintroductions into Europe. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 112(10), p. 3020–3025. doi: 10.1073/pnas.1412887112.
• Kay, Gemma L.; Sergeant, Martin J.; Giuffra, Valentina; Bandiera, Pasquale; Milanese, Marco & Bramanti, Barbara [Show all 8 contributors for this article] (2014). Recovery of a medieval Brucella melitensis genome using shotgun metagenomics. mBio. ISSN 2161-2129. 5(4). doi: 10.1128/mBio.01337-14.
• Bramanti, Barbara (2013). The Use of DNA Analysis in the Archaeology of Death and Buria. In Stutz, Liv Nilsson & Tarlow, Sarah (Ed.), The Oxford Handbook of the Archaeology of Death and Burial. Oxford University Press. ISSN 9780199569069. p. 99–122. doi: 10.1093/oxfordhb/9780199569069.013.0007.
• Harbeck, Michaela; Seifert, Lisa; Hänsch, Stephanie; Wagner, David; Birdsell, Dawn & Parise, Katy L. [Show all 14 contributors for this article] (2013). Yersinia pestis DNA from Skeletal Remains from the 6th Century AD Reveals Insights into Justinianic Plague. PLoS Pathogens. ISSN 1553-7366. 9(5). doi: 10.1371/journal.ppat.1003349. Full text in Research Archive

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• Stenseth, Nils Christian; Bramanti, Barbara; Büntgen, Ulf; Fell, Henry G.; Cohn, Samuel & Sebbane, Florent [Show all 10 contributors for this article] (2023). Reply to Alfani: Reconstructing past plague ecology to understand human history. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 120(11). doi: 10.1073/pnas.2300760120.
• Namouchi, Amine; Guellil, Meriam; Kersten, Oliver Sven; Hänsch, Stephanie; Ottoni, Claudio & Schmid, Boris Valentijn [Show all 16 contributors for this article] (2020). Correction for Namouchi et al., Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 17(22). doi: 10.1073/pnas.2007983117.
• Bramanti, Barbara; Namouchi, Amine; Schmid, Boris Valentijn; Dean, Katharine Rose & Stenseth, Nils Christian (2019). Reply to Barbieri et al.: Out of the Land of Darkness: Plague on the fur trade routes. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 116(16). doi: 10.1073/pnas.1902274116.
• Bramanti, Barbara; Namouchi, Amine; Schmid, Boris Valentijn; Dean, Katharine Rose & Stenseth, Nils Christian (2019). Out of the land of darkness: Plague on the fur trade routes. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 116(16), p. 7622–7623. doi: 10.1073/pnas.1902274116.
• Dean, Katharine Rose; Krauer, Fabienne; Walløe, Lars; Lingjærde, Ole Christian; Bramanti, Barbara & Stenseth, Nils Christian [Show all 7 contributors for this article] (2018). Reply to Park et al.: Human ectoparasite transmission of plague during the Second Pandemic is still plausible. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 115(34), p. E7894–E7895. doi: 10.1073/pnas.1810221115.
• Bramanti, Barbara (2014). Exploring Black Death mysteries in a new ancient DNA-lab.
• Bramanti, Barbara (2014). New genomic perspectives in historical plagues.
• Bramanti, Barbara (2014). The current genetic evidence for sites of origin of the three plague pandemics.
• Bramanti, Barbara (2014). Ancient DNA studies and the pandemics of the past.
• Bramanti, Barbara (2014). Inquiring into the Medieval Plagues.
• Bramanti, Barbara (2014). Yersin e oltre: 120 anni di studi biologici sulla peste e un nuovo progetto.
• Bramanti, Barbara & Hänsch, Stephanie (2014). Host-pathogens interactions: exploring the effects of epidemics on European human populations by means of ancient DNA analyses.
• Bramanti, Barbara (2014). Yersin and beyond: How can genomics and ecology help in understanding the history of plague?
• Bramanti, Barbara (2014). Was always ‘Better wed over the mixen than over the moor’?
• Bramanti, Barbara (2014). The medieval plagues: ecology, transmission modalities and routes of the infections.
• Bramanti, Barbara (2014). Ancient DNA of the European Hunter Gatherers.
• Bramanti, Barbara & Hänsch, Stephanie (2014). Was uns alte DNA zur Veränderung vergangener Ökosysteme mitteilen kann. Geographische Rundschau. ISSN 0016-7460.
• Riehm, Julia; Seifert, L; Wagner, D; Birdsell, Dawn; Thomas, A & Zoeller, L [Show all 14 contributors for this article] (2013). Yersinia pestis DNA from Skeletal Remains from the 6th Century AD Reveals Insights into Justinianic Plague.
• Schmid, Boris Valentijn; Buntgen, U; Easterday, William Ryan; Ginzler, Christian; Walløe, Lars & Bramanti, Barbara [Show all 7 contributors for this article] (2013). The pulse of Asia: The Black Death and successive reintroductions of plague into Europe.
• Bramanti, Barbara; Hänsch, Stephanie & Bogus, M (2013). Evolutionary consequences of the past pandemics. Ancient DNA: applications in human evolutionary history.
• Bramanti, Barbara (2013). The medieval plagues: can genetics and ecology help in understanding our history?
• Bramanti, Barbara (2013). MedPlag (2013-18): The medieval plagues: ecology, transmission modalities and routes of the infections – an ERC Advanced Grant.
• Bramanti, Barbara & Hänsch, Stephanie (2013). Paläogenetik der Pest: Gene, Gräber und Gebeine. Biologie in unserer Zeit. ISSN 0045-205X. 43(5), p. 300–305. doi: 10.1002/biuz.201310518.

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